FastOMA/nextflow.config at main · DessimozLab/FastOMA · GitHub

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// General configuration used in all profiles
manifest {
  name = "dessimozlab/FastOMA"
  description = """FastOMA computes Hierarchical Orthologous Groups from proteomes."""
  author = "Sina Majidian, Adrian Altenhoff"
  homePage = "https://omabrowser.org"
  mainScript = "FastOMA.nf"
  nextflowVersion = ">=22.10.4"
  defaultBranch = "main"
  doi = "10.1101/2024.01.29.577392"
  version = "0.6dev"
  contributors = [
        [
            name: 'Sina Majidian',
            affiliation: 'Johns Hopkins University; University of Lausanne',
            github: "https://github.com/sinamajidian",
            contribution: ['author', 'maintainer'],
            orcid: "https://orcid.org/0000-0001-5345-6982"
        ],
        [
            name: 'Adrian Altenhoff',
            affiliation: 'SIB Swiss Institute of Bioinformatics',
            github: 'https://github.com/alpae',
            contribution: ['author', 'maintainer'],
            orcid: 'https://orcid.org/0000-0001-7492-1273'
        ]
    ]
}

params {
  // default parameters for test run
  // these can be overridden by the user on the command line
  input           = null
  // input sub-folders, can also be somewhere else
  proteome_folder = null
  hogmap_in       = null
  splice_folder   = null
  species_tree    = null
  // cache path for (remote) archive input files
  test_data_cache = null
  // Keep deprecated parameter for backward compatibility
  input_folder = null

  // main output folder
  output_folder   = "Output"
  // output subfolder definition
  genetrees_folder = "${params.output_folder}/genetrees"
  msa_folder       = "${params.output_folder}/msa"
  hogmap_folder    = "${params.output_folder}/hogmap"
  temp_output      = "${params.output_folder}/temp_output" // temporary files for debugging

  // container settings
  container_name = "dessimozlab/fastoma"
  container_version = "dev"

  // OMAmer database for mapping to precomputed HOGs
  omamer_db = "https://omabrowser.org/All/LUCA.h5"

  // parameters for FastOMA
  filter_method = "col-row-threshold"
  filter_gap_ratio_row = 0.3
  filter_gap_ratio_col = 0.5
  nr_repr_per_hog = 5
  min_sequence_length = 20


  // other parameters
  debug_enabled = false   // generates additional files for debugging
  help = false            // prints help message
  write_msas = false      // store multiple sequence alignments of HOGs at each taxonomic level
  write_genetrees = false // store gene trees of HOGs at each taxonomic level
  force_pairwise_ortholog_generation = false  // force generation of pairwise orthologs even many species are present
  fasta_header_id_transformer = "noop"

  // statistics directory for reports by nextflow
  report = false // enable/disable report generation
  statsdir = "${params.output_folder}/stats"

  // configurations from nf-core for cluster specific settings
  custom_config_version   = "master"
  custom_config_base      = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  trace_report_suffix     = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')

  time_multiplier         = 1
  memory_multiplier       = 1
}


// Load base.config by default for all pipelines
includeConfig "conf/base.config"
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

profiles {
    debug {
        dumpHashes              = true
        process.beforeScript    = 'echo $HOSTNAME'
        cleanup                 = false
        nextflow.enable.configProcessNamesValidation = true
    }
    docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
        process.container       = "$params.container_name:$params.container_version"
    }
    arm {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled     = true
        singularity.autoMounts  = true
        process.container       = "$params.container_name:$params.container_version"
        conda.enabled           = false
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    apptainer {
        singularity.enabled     = false
        singularity.autoMounts  = false
        conda.enabled           = false
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        process.container       = "$params.container_name:$params.container_version"
    }
    conda {
        conda.enabled           = true
        conda.createTimeout     = '3 h'
        process.conda           = "${projectDir}/environment-conda.yml"
        singularity.enabled     = false
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    slurm {
        includeConfig 'conf/slurm_basic.config'
    }
    test      { includeConfig 'conf/test.config'          }
    large     { includeConfig 'conf/base_large.config'    }
    mammalia  { includeConfig 'conf/test-mammalia.config' }
    fungi     { includeConfig 'conf/test-fungi.config'    }
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

plugins {
    id 'nf-schema@2.4.0'
}

// Set schema validation options
validation {
    help { enabled = true }
}


// Creates logs for what, when, where, and how the workflow was run
timeline {
  enabled = !params.help && params.report
  file = "${params.statsdir}/timeline_${params.trace_report_suffix}.html"
  overwrite = true
}

report {
  enabled = !params.help && params.report
  file = "${params.statsdir}/report_${params.trace_report_suffix}.html"
  overwrite = true
}
trace {
    enabled = !params.help && params.report
    file    = "${params.statsdir}/trace_${params.trace_report_suffix}.txt"
    //fields = "task_id,native_id,hash,name,status,submit,complete,script"
    overwrite = true
}
dag {
    enabled = !params.help && params.report
    file    = "${params.statsdir}/pipeline_dag_${params.trace_report_suffix}.html"
    overwrite = true
}